PDBsum entry 1avd

Biotin-binding protein

PDB id: 1avd

Contents

Protein chains

123 a.a. *

Ligands

NAG

BTN ×2

Waters ×37

* Residue conservation analysis

PDB id:

1avd

Name:

Biotin-binding protein

Title:

Three-dimensional structure of the tetragonal crystal form of egg- white avidin in its functional complex with biotin at 2.7 angstroms resolution

Structure:

Avidin. Chain: a, b. Engineered: yes

Source:

Gallus gallus. Chicken. Organism_taxid: 9031

Biol. unit:

Tetramer (from PQS)

Resolution:

2.70Å R-factor: 0.174

Authors:

L.Pugliese,A.Coda,M.Malcovati,M.Bolognesi

Key ref:

L.Pugliese et al. (1993). Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution. J Mol Biol, 231, 698-710. PubMed id: 8515446

Date:

05-Mar-93 Release date: 31-Jan-94

Protein chains

P02701  (AVID_CHICK) -  Avidin from Gallus gallus

Seq: 152 a.a.

Struc: 123 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

J Mol Biol 231:698-710 (1993)

PubMed id: 8515446

Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution.

L.Pugliese, A.Coda, M.Malcovati, M.Bolognesi.

ABSTRACT

The three-dimensional structure of hen egg-white avidin, crystallized in a tetragonal crystal form, has been solved at 2.7 A resolution by molecular replacement methods. After refinement the crystallographic R-factor is 16.8%, for the 7255 reflections in the 10.0 to 2.7 A resolution range. The asymmetric unit contains two avidin polypeptide chains (M(r) 2 x 15,600), which build up the functional tetramer through a crystallographic 2-fold axis parallel to the c unit cell direction. The avidin tetramer has almost exact 222 molecular symmetry; the three possible dimers display quite distinct packing interfaces. Each protomer is organized in an eight-stranded antiparallel orthogonal beta-barrel, with extended loop regions. The avidin binding site within each promoter is located in a deep pocket, at the center of the barrel, displaying both hydrophobic and polar residues for recognition of the tightly bound vitamin. Two Trp residues, Trp70 and Trp97, and Phe79 are in close contact with biotin. Moreover, the binding pocket is partly closed in its outer rim by residue Trp110 of a neighboring subunit. Once bound, biotin is almost completely buried in the protein core, with the exception of the valeryl side-chain carboxylate group which is exposed to solvent, hydrogen bonds to residues Ala39, Thr40 and Ser75, and triggers the formation of a network of hydrogen bonded water molecules. Modeling of synthetic biotin analogues allows us to rationalize functional data available for the binding of these compounds, and to analyze them in terms of biotin recognition mechanism. Hen egg-white avidin shows clear structural homology to streptavidin, from Streptomyces avidinii, but significant deviations can be observed in some regions.